Generate Calibration Curve from specific samples (standard curve samples)

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Generate Calibration Curve from specific samples (standard curve samples) helmi  2025-05-27 03:22
 

Hello!

My lab made a standard curve mixing 4 different Ceramide Standards with the concentrations 100µM - 75µM - 50µM - 25µM - blank.
So I have 5 samples that were measured with an Obritrap, one sample called 100µM with 100µM of all of the 4 Ceramide Standards and the same for the rest.

I also have 6 biological samples that need to be quantified for Ceramides. They do not contain the standards.

I have been tasked with making a calibration curve to quantify the ceramides in the 6 biological samples.
Everything worked well with the transition list, importing results and setting up the calibration curve. The R-squared and calculated concentrations look fine but I worry that this method is not correct as the standards are not present in the biological samples but Skyline pretends that they are.

But when I add the concentrations of the ceramides to the Document Grid it fills in those concentrations for every molecule. And I cannot choose which calibration curve I want to use in the Document Grid.

I either need a "Surrogate Calibration Curve" / to choose with Calibration Curve to use or to choose from which molecules and samples the calibration curve should be created.
(Issue 964 Feature Request might work but I cannot find this in Skyline)

I use Skyline daily with the Molecule Interface.

Sorry for the long text

 
 
Nick Shulman responded:  2025-05-27 07:38
Here is the help page for surrogate standards and surrogate calibration curves:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=Surrogate%20Standards

For a simple dilution series you set the "Analyte Concentration" on each Replicate. If your different standards had different starting concentrations then you might also set the "Concentration Multiplier" on each Molecule so that the Concentration Multiplier times the Analyte Concentration is the actual concentration of that standard molecule in that Replicate.
If your dilution series was more complicated than that, you can instead set the "Explicit Standard Concentration" value on each Molecule Result.
In order to be able to set values like "Concentration Multiplier" and "Explicit Standard Concentration" you will need to create a Custom Report which includes those columns.
You can learn about Custom Reports here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

There is a binoculars button at the top of the Customize Report dialog which will allow you to search for a particular column by name.
-- Nick